In [1]:
# run this cell first to set up appropriate objects
import os
token = os.environ["KB_AUTH_TOKEN"]
# these are for client-server communication
from doekbase.data_api.annotation.genome_annotation.api import GenomeAnnotationClientAPI
from doekbase.data_api.taxonomy.taxon.api import TaxonClientAPI
from doekbase.data_api.sequence.assembly.api import AssemblyClientAPI
# the ObjectClientAPI is not ready yet, coming soon
taxonurl='https://ci.kbase.us/services/data/taxon'
assemblyurl='https://ci.kbase.us/services/data/assembly'
genomeannotationurl='https://ci.kbase.us/services/data/genome_annotation'
# hard-coded workspace reference for now, an arabidopsis genome
ref='2844/12'
ref="ReferenceEnsemblPlantGenomeAnnotations/3847_EnsembleRelease30"
In [17]:
annoapi = GenomeAnnotationClientAPI(genomeannotationurl, token, ref)
print "new annotation client"
assemblyref = annoapi.get_assembly()
print "assembly "+assemblyref
assemblyapi = AssemblyClientAPI(assemblyurl, token, assemblyref)
contigs = assemblyapi.get_contig_ids()
contig_lens = assemblyapi.get_contig_lengths()
contig_lens_vals = contig_lens.values()
contig_lens_vals_log10 = [math.log10(float(i)) for i in contig_lens_vals]
gc = assemblyapi.get_contig_gc_content()
gc_vals = gc.values()
#print contig_lengths.values()
new annotation client
assembly 4435/72/2
In [39]:
from plotly import __version__
from plotly.offline import download_plotlyjs, init_notebook_mode, iplot
from plotly.graph_objs import *
import numpy as np
import pandas as pd
import math
print __version__ # requires version >= 1.9.0
init_notebook_mode()
iplot({"data":[Histogram2dContour(x=contig_lens_vals_log10, y=gc_vals, contours=Contours(coloring='heatmap')),
Scatter(x=contig_lens_vals_log10, y=gc_vals, mode='markers', marker=Marker(color='white', size=3, opacity=0.3))],
"layout": Layout(xaxis=XAxis(title='Contig Lengths (log10)', type='log'), yaxis=YAxis(title='%GC'))
}, show_link=False)
#'layout': Layout(yaxis=YAxis(title='%GC'), xaxis=XAxis(title='Contig length (bp)'), type='log'), show_link=False)
#,
# Scatter(x=x, y=y, mode='markers', marker=Marker(color='white', size=3, opacity=0.3))
1.9.5
In [30]:
import pandas as pd
iplot({
'data': [
Scatter(x=df[continent+'_Life Expentancy [in years]'],
y=df[continent+'_Gross Domestic Product per Capita [in USD of the year 2000]'],
text=df[continent+'_text'],
marker=Marker(size=df[continent+'_marker.size'], sizemode='area', sizeref=131868,),
mode='markers',
name=continent) for continent in ['Africa', 'Americas', 'Asia', 'Europe', 'Oceania']
],
'layout': Layout(xaxis=XAxis(title='Life Expectancy'), yaxis=YAxis(title='GDP per Capita', type='log'))
}, show_link=False)
#Layout(xaxis=XAxis(title='Life Expectancy'), yaxis=YAxis(title='GDP per Capita', type='log')
---------------------------------------------------------------------------
NameError Traceback (most recent call last)
<ipython-input-30-d5923120b32a> in <module>()
8 marker=Marker(size=df[continent+'_marker.size'], sizemode='area', sizeref=131868,),
9 mode='markers',
---> 10 name=continent) for continent in ['Africa', 'Americas', 'Asia', 'Europe', 'Oceania']
11 ],
12 'layout': Layout(xaxis=XAxis(title='Life Expectancy'), yaxis=YAxis(title='GDP per Capita', type='log'))
NameError: name 'df' is not defined
In [37]:
contig_lens_vals_log10
Out[37]:
[3.8212514315459414,
3.474653253362063,
3.2195845262142546,
5.243434936520088,
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